If your selling prices are set to GST Exclusive in Admin / Defaults / Manage Product Defaults a calculation error means setting the CC code up in Financial Defaults will add GST twice.
As an alternative:
Set up a product code "CC" – set the sales G/L to Bank Fees in the Settings Tab. (alternatively you could also code it to the same G/L as your merchant fees– it would contra against the merchant fee expenses therefore you can track how much you are recovering by adding the surcharge).
When taking payment by credit card, add a product line CC and enter quantity = 0.03 (for 3%) and rate = the GST Exclusive amount from the invoice footer as shown below.